[galaxy-user] SNPeff tool?
Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SNPeff tool?
Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SNPeff tool?
I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SNPeff tool?
Hi, Yes, I see that you can generate the VCF files that way but there is no seamless way of doing it entirely from within galaxy - i.e. you need to come out of galaxy at some point (or am I missing something?). Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 14:39, Chorny, Ilya wrote: I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy
Re: [galaxy-user] SNPeff tool?
Gatk unified genotyper will take a bam/Sam and generate a vcf. Sent from my iPhone On Nov 8, 2011, at 6:54 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, Yes, I see that you can generate the VCF files that way but there is no seamless way of doing it entirely from within galaxy - i.e. you need to come out of galaxy at some point (or am I missing something?). Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 14:39, Chorny, Ilya wrote: I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy
